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Anatomical and Pathological Observation and Analysis of SARS and COVID-19: Microthrombosis Is the Main Cause of Death Biol. Proced. Online (IF 2.711) Pub Date : 2021-01-20 Wenjing Chen; Jing Ye Pan
The spread of the coronavirus (SARS-CoV-2, COVID-19 for short) has caused a large number of deaths around the world. We summarized the data reported in the past few months and emphasized that the main causes of death of COVID-19 patients are DAD (Diffuse Alveolar Damage) and DIC (Disseminated intravascular coagulation). Microthrombosis is a prominent clinical feature of COVID-19, and 91.3% of dead
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A Novel PCR Method for Detecting ACE Gene Insertion/Deletion Polymorphisms and its Clinical Application Biol. Proced. Online (IF 2.711) Pub Date : 2021-01-07 Xue-min Yang; Jian-ping Liang; Xiao-juan Huang; Xiang-rong Wang; Yang Sun; Chen Dong; Ya-li Cui; Wen-li Hui
Angiotensin-converting enzyme (ACE) plays a major role in blood pressure regulation and cardiovascular homeostasis. The wide distribution and multifunctional properties of ACE suggest it’s involvement in various pathophysiological conditions. In this study, a novel visual detection method for ACE I/D polymorphisms was designed by integrating direct PCR without the need for DNA extraction using gold
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Development of a Novel Orthotopic Gastric Cancer Mouse Model Biol. Proced. Online (IF 2.711) Pub Date : 2021-01-04 Wonyoung Kang; Leigh Maher; Michael Michaud; Seong-Woo Bae; Seongyeong Kim; Hye Seung Lee; Seock-Ah Im; Han-Kwang Yang; Charles Lee
Gastric cancer metastasis is a highly fatal disease with a five-year survival rate of less than 5%. One major obstacle in studying gastric cancer metastasis is the lack of faithful models available. The cancer xenograft mouse models are widely used to elucidate the mechanisms of cancer development and progression. Current procedures for creating cancer xenografts include both heterotopic (i.e., subcutaneous)
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Mutational Analysis of Ocriplasmin to Reduce Proteolytic and Autolytic Activity in Pichia pastoris Biol. Proced. Online (IF 2.711) Pub Date : 2020-12-13 Roghayyeh Baghban; Safar Farajnia; Younes Ghasemi; Reyhaneh Hoseinpoor; Azam Safary; Mojtaba Mortazavi; Nosratollah Zarghami
Ocriplasmin (Jetrea) is using for the treatment of symptomatic vitreomacular adhesion. This enzyme undergoes rapid inactivation and limited activity duration as a result of its autolytic nature after injection within the eye. Moreover, the proteolytic activity can cause photoreceptor damage, which may result in visual impairment in more serious cases. The present research aimed to reduce the disadvantages
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Correction to: CRISPR-Based Diagnosis of Infectious and Noninfectious Diseases Biol. Proced. Online (IF 2.711) Pub Date : 2020-11-07 Somayeh Jolany vangah; Camellia Katalani; Hannah A. Boone; Abbas Hajizade; Adna Sijercic; Gholamreza Ahmadian
An amendment to this paper has been published and can be accessed via the original article.
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Molecular contribution of BRCA1 and BRCA2 to genome instability in breast cancer patients: review of radiosensitivity assays Biol. Proced. Online (IF 2.711) Pub Date : 2020-10-01 Fatemeh Sadeghi; Marzieh Asgari; Mojdeh Matloubi; Maral Ranjbar; Nahid Karkhaneh Yousefi; Tahereh Azari; Majid Zaki-Dizaji
DNA repair pathways, cell cycle arrest checkpoints, and cell death induction are present in cells to process DNA damage and prevent genomic instability caused by various extrinsic and intrinsic ionizing factors. Mutations in the genes involved in these pathways enhances the ionizing radiation sensitivity, reduces the individual’s capacity to repair DNA damages, and subsequently increases susceptibility
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CRISPR-Based Diagnosis of Infectious and Noninfectious Diseases. Biol. Proced. Online (IF 2.711) Pub Date : 2020-09-14 Somayeh Jolany Vangah,Camellia Katalani,Hannah A Booneh,Abbas Hajizade,Adna Sijercic,Gholamreza Ahmadian
Interest in CRISPR technology, an instrumental component of prokaryotic adaptive immunity which enables prokaryotes to detect any foreign DNA and then destroy it, has gained popularity among members of the scientific community. This is due to CRISPR’s remarkable gene editing and cleaving abilities. While the application of CRISPR in human genome editing and diagnosis needs to be researched more fully
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Potential Diagnostic Systems for Coronavirus Detection: a Critical Review. Biol. Proced. Online (IF 2.711) Pub Date : 2020-09-01 Elena Ekrami,Mahdi Pouresmaieli,Fatemeh Barati,Sahar Asghari,Farzad Ramezani Ziarani,Parvin Shariati,Matin Mamoudifard
Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment
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Development of an In Vitro 3D Model for Investigating Ligamentum Flavum Hypertrophy. Biol. Proced. Online (IF 2.711) Pub Date : 2020-09-01 Cheng-Li Lin,Yi-Ting Kuo,Che-Hao Tsao,Yan-Jye Shyong,Shu-Hsien Shih,Ting-Yuan Tu
Ligamentum flavum hypertrophy (LFH) is among the most crucial factors in degenerative lumbar spinal stenosis, which can cause back pain, lower extremity pain, cauda equina syndrome and neurogenic claudication. The exact pathogenesis of LFH remains elusive despite extensive research. Most in vitro studies investigating LFH have been carried out using conventional two-dimensional (2D) cell cultures,
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A comprehensive review of COVID-19 characteristics. Biol. Proced. Online (IF 2.711) Pub Date : 2020-08-04 Hanie Esakandari,Mohsen Nabi-Afjadi,Javad Fakkari-Afjadi,Navid Farahmandian,Seyed-Mohsen Miresmaeili,Elham Bahreini
In December 2019, a novel coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or (2019-nCoV) with unknown origin spread in Hubei province of China. The epidemic disease caused by SARS-CoV-2 called coronavirus disease-19 (COVID-19). The presence of COVID-19 was manifested by several symptoms, ranging from asymptomatic/mild symptoms to severe illness and death. The viral infection
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Isolation and Quantification of Blood Apoptotic Bodies, a Non-invasive Tool to Evaluate Apoptosis in Patients with Ischemic Stroke and Neurodegenerative Diseases. Biol. Proced. Online (IF 2.711) Pub Date : 2020-08-01 Gemma Serrano-Heras,Inmaculada Díaz-Maroto,Beatriz Castro-Robles,Blanca Carrión,Ana B Perona-Moratalla,Julia Gracia,Sandra Arteaga,Francisco Hernández-Fernández,Jorge García-García,Oscar Ayo-Martín,Tomás Segura
Improper regulation of apoptosis has been postulated as one of the main factors that contributes to the etiology and/or progression of several prevalent diseases, including ischemic stroke and neurodegenerative pathologies. Consequently, in the last few years, there has been an ever-growing interest in the in vivo study of apoptosis. The clinical application of the tissue sampling and imaging approaches
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Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients. Biol. Proced. Online (IF 2.711) Pub Date : 2020-07-25 Flavio De Maio,Brunella Posteraro,Francesca Romana Ponziani,Paola Cattani,Antonio Gasbarrini,Maurizio Sanguinetti
We analyzed the bacterial communities of the nasopharynx in 40 SARS-CoV-2 infected and uninfected patients. All infected patients had a mild COVID-19 disease. We did not find statistically significant differences in either bacterial richness and diversity or composition. These findings suggest a nasopharyngeal microbiota at least early resilient to SARS-CoV-2 infection.
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Expansion of Single Cell Transcriptomics Data of SARS-CoV Infection in Human Bronchial Epithelial Cells to COVID-19. Biol. Proced. Online (IF 2.711) Pub Date : 2020-07-23 Reza Zolfaghari Emameh,Hassan Nosrati,Mahyar Eftekhari,Reza Falak,Majid Khoshmirsafa
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19) that was emerged as a new member of coronaviruses since December 2019 in Wuhan, China and then after was spread in all continentals. Since SARS-CoV-2 has shown about 77.5% similarity to SARS-CoV, the transcriptome and immunological regulations of SARS-CoV-2 was expected to have high
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Potential Drugs and Remedies for the Treatment of COVID-19: a Critical Review. Biol. Proced. Online (IF 2.711) Pub Date : 2020-07-23 Fatemeh Barati,Mahdi Pouresmaieli,Elena Ekrami,Sahar Asghari,Farzad Ramezani Ziarani,Matin Mamoudifard
COVID-19 disease with a high rate of contagious and highly nonspecific symptoms, is an infectious disease caused by a newly discovered coronavirus. Most people who fall sick with COVID-19 will experience mild to moderate symptoms such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia and recover without any special cure. However, some others need special and emergency treatment to
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Efficient In Vivo Introduction of Point Mutations Using ssODN and a Co-CRISPR Approach. Biol. Proced. Online (IF 2.711) Pub Date : 2020-07-14 Tgst Levi,Anna Sloutskin,Rachel Kalifa,Tamar Juven-Gershon,Offer Gerlitz
The generation of point mutations is a major tool for evaluating the roles of specific nucleotides or amino acids within the regulatory or functional landscape. However, examination of these mutations in vivo requires the generation of animals carrying only the relevant point mutations at the endogenous genomic loci, which is technically challenging. The CRISPR-Cas9 based genome editing greatly facilitates
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Bimodal Whole-Mount Imaging of Tendon Using Confocal Microscopy and X-ray Micro-Computed Tomography. Biol. Proced. Online (IF 2.711) Pub Date : 2020-07-01 Neil Marr,Mark Hopkinson,Andrew P Hibbert,Andrew A Pitsillides,Chavaunne T Thorpe
Three-dimensional imaging modalities for optically dense connective tissues such as tendons are limited and typically have a single imaging methodological endpoint. Here, we have developed a bimodal procedure utilising fluorescence-based confocal microscopy and x-ray micro-computed tomography for the imaging of adult tendons to visualise and analyse extracellular sub-structure and cellular composition
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Combination of Size-Exclusion Chromatography and Ultracentrifugation Improves the Proteomic Profiling of Plasma-Derived Small Extracellular Vesicles. Biol. Proced. Online (IF 2.711) Pub Date : 2020-06-23 Rui Wei,Libo Zhao,Guanyi Kong,Xiang Liu,Shengtao Zhu,Shutian Zhang,Li Min
Circulating small extracellular vesicles (sEVs) and its associated proteins are of great interest in the early detection of many diseases. However, there is no gold standard for plasma sEVs isolation, especially for proteomic profiling which could be largely affected by contamination such as lipoproteins and plasma proteins. Previous studies suggested combinations of different sEVs isolation methods
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Application of System Biology to Explore the Association of Neprilysin, Angiotensin-Converting Enzyme 2 (ACE2), and Carbonic Anhydrase (CA) in Pathogenesis of SARS-CoV-2. Biol. Proced. Online (IF 2.711) Pub Date : 2020-06-19 Reza Zolfaghari Emameh,Reza Falak,Elham Bahreini
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears with common symptoms including fever, dry cough, and fatigue, as well as some less common sysmptoms such as loss of taste and smell, diarrhea, skin rashes and discoloration of fingers. COVID-19 patients may also suffer from serious symptoms including shortness of breathing, chest pressure
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Deep Insights in Circular RNAs: from biogenesis to therapeutics. Biol. Proced. Online (IF 2.711) Pub Date : 2020-05-15 Peerzada Tajamul Mumtaz,Qamar Taban,Mashooq Ahmad Dar,Shabir Mir,Zulfkar Ul Haq,Sajad Majeed Zargar,Riaz Ahmad Shah,Syed Mudasir Ahmad
Circular RNAs (circRNAs) have emerged as a universal novel class of eukaryotic non-coding RNA (ncRNA) molecules and are becoming a new research hotspot in RNA biology. They form a covalent loop without 5′ cap and 3′ tail, unlike their linear counterparts. Endogenous circRNAs in mammalian cells are abundantly conserved and discovered so far. In the biogenesis of circRNAs exonic, intronic, reverse complementary
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Reverse Genetics Assembly of Newcastle Disease Virus Genome Template Using Asis-Sal-Pac BioBrick Strategy. Biol. Proced. Online (IF 2.711) Pub Date : 2020-05-01 Amin Tavassoli,Safoura Soleymani,Alireza Haghparast,Gholamreza Hashemi Tabar,Mohammad Reza Bassami,Hesam Dehghani
The BioBrick construction as an approach in synthetic biology provides the ability to assemble various gene fragments. To date, different BioBrick strategies have been exploited for assembly and cloning of a variety of gene fragments. We present a new BioBrick strategy, here referred as Asis-Sal-Pac BioBrick, which we used for the assembly of NDV as a candidate for single-stranded non-segmented, negative-sense
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Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient. Biol. Proced. Online (IF 2.711) Pub Date : 2020-04-21 Reza Zolfaghari Emameh,Hassan Nosrati,Ramezan Ali Taheri
Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical
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Caco-2 Cells for Measuring Intestinal Cholesterol Transport - Possibilities and Limitations. Biol. Proced. Online (IF 2.711) Pub Date : 2020-04-11 Verena Hiebl,Daniel Schachner,Angela Ladurner,Elke H Heiss,Herbert Stangl,Verena M Dirsch
The human Caco-2 cell line is a common in vitro model of the intestinal epithelial barrier. As the intestine is a major interface in cholesterol turnover and represents a non-biliary pathway for cholesterol excretion, Caco-2 cells are also a valuable model for studying cholesterol homeostasis, including cholesterol uptake and efflux. Currently available protocols are, however, either sketchy or not
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High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections – Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils Biol. Proced. Online (IF 2.711) Pub Date : 2020-03-15 Niina Aaltonen; Prosanta K. Singha; Hermina Jakupović; Thomas Wirth; Haritha Samaranayake; Sanna Pasonen-Seppänen; Kirsi Rilla; Markku Varjosalo; Laura E. Edgington-Mitchell; Paulina Kasperkiewicz; Marcin Drag; Sara Kälvälä; Eemeli Moisio; Juha R. Savinainen; Jarmo T. Laitinen
Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue
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Adjuvant Chemotherapy with Chinese Herbal Medicine Formulas Versus Placebo in Patients with Lung Adenocarcinoma after Radical Surgery: a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial Biol. Proced. Online (IF 2.711) Pub Date : 2020-03-01 Qin Wang; Lijing Jiao; Shengfei Wang; Peiqi Chen; Ling Bi; Di Zhou; Jialin Yao; Jiaqi Li; Liyu Wang; Zhiwei Chen; Yingjie Jia; Ziwen Zhang; Weisheng Shen; Weirong Zhu; Jianfang Xu; Yong Gao; Ling Xu; Yabin Gong
The toxicity and side effects caused by adjuvant chemotherapy (ACT) after radical surgery for lung adenocarcinoma (LAC) lead to early termination frequently. This study was conducted to provide an objective basis for the effect of Chinese herbal medicine formulas (CHMFs) combined with chemotherapy in reducing toxicity and enhancing efficacy of ACT. From February 17th, 2012 to March 20th, 2015, 233
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Exploring G Protein-Coupled Receptor Signaling in Primary Pancreatic Islets. Biol. Proced. Online (IF 2.711) Pub Date : 2020-02-15 Juliane Röthe,Robert Kraft,Torsten Schöneberg,Doreen Thor
Targeting G protein-coupled receptors (GPCRs) in pancreatic cells is feasible to modulate glucose-induced insulin secretion. Because pancreatic islets consist of several cell types and GPCRs can couple to more than one G-protein family, results obtained in pancreatic cell lines do not always match the response in primary cells or intact islets. Therefore, we set out to establish a protocol to analyze
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A microcarrier-based spheroid 3D invasion assay to monitor dynamic cell movement in extracellular matrix. Biol. Proced. Online (IF 2.711) Pub Date : 2020-02-01 Hui Liu,Tao Lu,Gert-Jan Kremers,Ann L B Seynhaeve,Timo L M Ten Hagen
Cell invasion through extracellular matrix (ECM) is a critical step in tumor metastasis. To study cell invasion in vitro, the internal microenvironment can be simulated via the application of 3D models. This study presents a method for 3D invasion examination using microcarrier-based spheroids. Cell invasiveness can be evaluated by quantifying cell dispersion in matrices or tracking cell movement through
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Analytical Validation of Telomere Analysis Technology® for the High-Throughput Analysis of Multiple Telomere-Associated Variables. Biol. Proced. Online (IF 2.711) Pub Date : 2020-01-15 Nuria de Pedro,María Díez,Irene García,Jorge García,Lissette Otero,Luis Fernández,Beatriz García,Rut González,Sara Rincón,Diego Pérez,Estefanía Rodríguez,Enrique Segovia,Pilar Najarro
A large number of studies have suggested a correlation between the status of telomeres and disease risk. High-throughput quantitative fluorescence in situ hybridization (HT Q-FISH) is a highly accurate telomere measurement technique that can be applied to the study of large cell populations. Here we describe the analytical performance testing and validation of Telomere Analysis Technology (TAT®), a
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Glycosaminoglycans from Co-Products of «Scyliorhinus canicula»: Extraction and Purification in Reference to the European Pharmacopoeia Requirement Biol. Proced. Online (IF 2.711) Pub Date : 2020-01-02 Nawras Talmoudi; Noureddine Ghariani; Saloua Sadok
Glycosaminoglycans (GAGs), including hyaluronic acid (HA), dermatan sulfate (DS) and chondroitin sulfate (CS) are essential components of the bone and cartilage tissues. CS isolated from the cartilage tissue of various animals has found application in pharmaceuticals, cosmetics and food industries. In the first part of the present work, three methods were used and compared to extract and purify glycosaminoglycans
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Bone Marrow-Derived Mesenchymal Stem Cells Modified with Akt1 Ameliorates Acute Liver GVHD Biol. Proced. Online (IF 2.711) Pub Date : 2019-12-16 Lukun Zhou; Shuang Liu; Zhao Wang; Jianfeng Yao; Wenbin Cao; Shulian Chen; Wenjun Xie; Shuqing Feng; Yuanfu Xu; Tao Cheng; Mingzhe Han; Sizhou Feng
Liver injury associated with acute graft-versus-host disease (aGVHD) is a frequent and severe complication of hematopoietic stem cell transplantation and remains a major cause of transplant-related mortality. Bone marrow-derived mesenchymal stem cells (BM-MSCs) has been proposed as a potential therapeutic approach for aGVHD. However, the therapeutic effects are not always achieved. In this study, we
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Cell-Wide Survey of Amide-Bonded Lysine Modifications by Using Deacetylase CobB Biol. Proced. Online (IF 2.711) Pub Date : 2019-12-01 Yun Wei; Wan-Jie Yang; Qi-Jun Wang; Peng-Cheng Lin; Jian-Yuan Zhao; Wei Xu; Shi-Min Zhao; Xia-Di He
Lysine post-translational modifications are important regulators of protein function. Proteomic and biochemical approaches have resulted in identification of several lysine modifications, including acetylation, crotonylation, and succinylation. Here, we developed an approach for surveying amide-bonded lysine modifications in the proteome of human tissues/cells based on the observation that many lysine
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Application of a New Multiplexed Array for Rapid, Sensitive, Simultaneous and Quantitative Assessment of Spliced and Unspliced XBP1 Biol. Proced. Online (IF 2.711) Pub Date : 2019-11-15 Stuart Creedican; Aaron Talty; Stephen P. Fitzgerald; Afshin Samali; Ciarán Richardson; Adrienne M. Gorman; Kenneth Martin
IRE1α-mediated unconventional splicing of XBP1 is emerging as a biomarker in several disease states and is indicative of activation of the unfolded protein response sensor IRE1. Splicing of XBP1 mRNA results in the translation of two distinct XBP1 protein isoforms (XBP1s and XBP1u) which, due to post-translational regulation, do not correlate with mRNA levels. As both XBP1 isoforms are implicated in
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Manipulating osa-MIR156f Expression by D18 Promoter to Regulate Plant Architecture and Yield Traits both in Seasonal and Ratooning Rice. Biol. Proced. Online (IF 2.711) Pub Date : 2019-11-04 Qing Liu,Yi Su,Yunhua Zhu,Keqin Peng,Bin Hong,Ruozhong Wang,Mahmoud Gaballah,Langtao Xiao
Rice (Oryza sativa L.) feeds more than half of the world’s population. Ratooning rice is an economical alternative to the second seasonal rice, thus increasing the yield of ratooning rice is highly important. Here we report an applicable transgenic line constructed through the manipulation of osa-MIR156f expression in rice shoot using the OsGA3ox2 (D18) promoter. In seasonal rice, the D18–11 transgenic
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Optimization of Immunofluorescent Detection of Bone Marrow Disseminated Tumor Cells. Biol. Proced. Online (IF 2.711) Pub Date : 2018-07-11 Haley D Axelrod,Kenneth J Pienta,Kenneth C Valkenburg
Background Cancer metastasis is the primary cause of cancer-related deaths and remains incurable. Current clinical methods for predicting metastatic recurrence are not sensitive enough to detect individual cancer cells in the body; therefore, current efforts are directed toward liquid biopsy-based assays to capture circulating and disseminated tumor cells (CTCs and DTCs) in the blood and bone marrow
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Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin. Biol. Proced. Online (IF 2.711) Pub Date : 2018-06-09 Utkarsha A Singh,Mukta Kumari,Soumya Iyengar
Background Although genomic DNA isolation using the Chelex 100 resin is rapid and inexpensive, the DNA obtained by this method has a low concentration in solution and contains suspended impurities. The presence of debris in the DNA solution may result in degradation of DNA on long term storage and inhibition of the polymerase chain reaction. In order to remove impurities and concentrate the DNA in
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Isolation and Semi Quantitative PCR of Na+/H+ Antiporter (SOS1 and NHX) Genes under Salinity Stress in Kochia scoparia. Biol. Proced. Online (IF 2.711) Pub Date : 2018-06-09 Leila Fahmideh,Ziba Fooladvand
Background Kochia scoparia is a dicotyledonous annual herb and belongs to the Amaranthaceae family. Genetic diversity and resistance to drought stress of this plant has made it widely scattered in different regions which contains highly genetic diversity and great potential as fodder and can grow on salty, drought affected areas. Since the soil salinity has become widely spread, environmental concern
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Blockade of ITGA2 Induces Apoptosis and Inhibits Cell Migration in Gastric Cancer. Biol. Proced. Online (IF 2.711) Pub Date : 2018-05-11 Yu-Chang Chuang,Hsin-Yi Wu,Yu-Ling Lin,Shey-Cherng Tzou,Cheng-Hsun Chuang,Ting-Yan Jian,Pin-Rong Chen,Yuan-Ching Chang,Chi-Hsin Lin,Tse-Hung Huang,Chao-Ching Wang,Yi-Lin Chan,Kuang-Wen Liao
Background Gastric cancer is currently the fourth leading cause of cancer-related death worldwide. Gastric cancer is often diagnosed at advanced stages and the outcome of the treatment is often poor. Therefore, identifying new therapeutic targets for this cancer is urgently needed. Integrin alpha 2 (ITGA2) subunit and the beta 1 subunit form a heterodimer for a transmembrane receptor for extracellular
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Use of RNA Immunoprecipitation Method for Determining Sinorhizobium meliloti RNA-Hfq Protein Associations In Vivo. Biol. Proced. Online (IF 2.711) Pub Date : 2018-05-11 Mengsheng Gao,Anne Benge,Julia M Mesa,Regina Javier,Feng-Xia Liu
Background Soil bacterium Sinorhizobium meliloti (S. meliloti) forms an endosymbiotic partnership with Medicago truncatula (M. truncatula) roots which results in root nodules. The bacteria live within root nodules where they function to fix atmospheric N2 and supply the host plant with reduced nitrogen. The bacterial RNA-binding protein Hfq (Hfq) is an important regulator for the effectiveness of the
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DNA Area and NETosis Analysis (DANA): a High-Throughput Method to Quantify Neutrophil Extracellular Traps in Fluorescent Microscope Images. Biol. Proced. Online (IF 2.711) Pub Date : 2018-04-06 Ryan Rebernick,Lauren Fahmy,Christopher Glover,Mandar Bawadekar,Daeun Shim,Caitlyn L Holmes,Nicole Rademacher,Hemanth Potluri,Christie M Bartels,Miriam A Shelef
Background Neutrophil extracellular traps (NETs), extracellular structures composed of decondensed chromatin and antimicrobial molecules, are released in a process called NETosis. NETs, which are part of normal host defense, have also been implicated in multiple human diseases. Unfortunately, methods for quantifying NETs have limitations which constrain the study of NETs in disease. Establishing optimal
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Treatment of Advanced Non-small-Cell Lung Cancer with Qi-Nourishing Essence-Replenishing Chinese Herbal Medicine Combined with Chemotherapy. Biol. Proced. Online (IF 2.711) Pub Date : 2018-04-06 Yabin Gong,Zhenye Xu,Changjuan Jin,Haibin Deng,Zhongqi Wang,Weidong Zhou,Ming Zhang,Xiaozhen Zhao,Lifang Wang
Background To evaluate the effect of qi-nourishing essence-replenishing Chinese herbal medicine combined with chemotherapy in survival of advanced non-small-cell lung cancer(NSCLC) patients with essence and qi deficiency. Methods A prospective multi-centered randomized controlled study was conducted, and 266 advanced NSCLC patients were enrolled. 126 patients in control group received Vinorelbine plus
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High-Sensitivity and High-Resolution In Situ Hybridization of Coding and Long Non-coding RNAs in Vertebrate Ovaries and Testes. Biol. Proced. Online (IF 2.711) Pub Date : 2018-03-07 Natsumi Takei,Takuma Nakamura,Shohei Kawamura,Yuki Takada,Yui Satoh,Atsushi P Kimura,Tomoya Kotani
Background Subcellular localization of coding and non-coding RNAs has emerged as major regulatory mechanisms of gene expression in various cell types and many organisms. However, techniques that enable detection of the subcellular distribution of these RNAs with high sensitivity and high resolution remain limited, particularly in vertebrate adult tissues and organs. In this study, we examined the expression
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Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results. Biol. Proced. Online (IF 2.711) Pub Date : 2018-03-07 Shitao Zhao,Jianqiang Sun,Kentaro Shimizu,Koji Kadota
Background Hierarchical Sample clustering (HSC) is widely performed to examine associations within expression data obtained from microarrays and RNA sequencing (RNA-seq). Researchers have investigated the HSC results with several possible criteria for grouping (e.g., sex, age, and disease types). However, the evaluation of arbitrary defined groups still counts in subjective visual inspection. Results
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Visualisation of Multiple Tight Junctional Complexes in Human Airway Epithelial Cells. Biol. Proced. Online (IF 2.711) Pub Date : 2018-02-13 Alysia G Buckley,Kevin Looi,Thomas Iosifidis,Kak-Ming Ling,Erika N Sutanto,Kelly M Martinovich,Elizabeth Kicic-Starcevich,Luke W Garratt,Nicole C Shaw,Francis J Lannigan,Alexander N Larcombe,Graeme Zosky,Darryl A Knight,Paul J Rigby,Anthony Kicic,Stephen M Stick
Background Apically located tight junctions in airway epithelium perform a fundamental role in controlling macromolecule migration through paracellular spaces. Alterations in their expression may lead to disruptions in barrier integrity, which subsequently facilitates entry of potential bacterial and other pathogens into the host. Furthermore, there is emerging evidence that the barrier integrity of
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Antitumor Efficacy of Human Monocyte-Derived Dendritic Cells: Comparing Effects of two Monocyte Isolation Methods. Biol. Proced. Online (IF 2.711) Pub Date : 2018-02-13 Graça S Marques,Zélia Silva,Paula A Videira
Background Dendritic cells (DCs), which can be used as anti-cancer vaccines, are generally obtained in vitro from isolated CD14+ monocytes (MoDCs). This generates high cell numbers and allows instructing DCs to guarantee effective antitumor responses. However, the impact of the monocyte isolation step in the antitumor effectiveness of the generated MoDCs is still unknown. Here, we compared the most
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Gibson Deletion: a novel application of isothermal in vitro recombination. Biol. Proced. Online (IF 2.711) Pub Date : 2018-01-30 Swara Kalva,Jef D Boeke,Paolo Mita
Background Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a "custom DNA" molecule, the isothermal in vitro assembly, or Gibson assembly, allows for an efficient, one-step, scarless recombination-based assembly. Results Here, we apply and characterize the use of Gibson assembly for the deletion
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Cancer chemoprevention and therapy using chinese herbal medicine. Biol. Proced. Online (IF 2.711) Pub Date : 2018-01-13 Lijing Jiao,Ling Bi,Yan Lu,Qin Wang,Yabin Gong,Jun Shi,Ling Xu
Traditional Chinese medicine (TCM) plays an indispensable role in cancer prevention and treatment. Chinese herbal medicine (CHM) is a key component of TCM and has been practiced for thousands of years. A number of naturally occurring products from Chinese herbs extracts exhibit strong inhibitory properties against carcinogenesis, including CHM single-herb extracts, CHM-derived active components, and
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Maintaining RNA Integrity for Transcriptomic Profiling of Ex Vivo Cultured Limbal Epithelial Stem Cells after Fluorescence-Activated Cell Sorting (FACS). Biol. Proced. Online (IF 2.711) Pub Date : 2017-12-20 Lei Liu,Frederik Mølgaard Nielsen,Simone Elkjær Riis,Jeppe Emmersen,Trine Fink,Jesper Østergaard Hjortdal,Chris Bath,Vladimir Zachar
Background Transcriptomic profiling of ex vivo cultured human limbal epithelial stem cells (hLESCs) will foster better understanding of corneal physiology and novel treatment paradigms to limbal stem cell deficiency (LSCD). However, currently such profiling studies are hampered due to difficulties with producing sufficient amounts of intact mRNA for deep RNA sequencing (RNA-seq) from subpopulations
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Production of Monoclonal Antibodies against Human Trefoil Factor 3 and Development of a Modified-Sandwich ELISA for Detection of Trefoil Factor 3 Homodimer in Saliva. Biol. Proced. Online (IF 2.711) Pub Date : 2017-11-21 Saichit Khummuang,Waraporn Phanphrom,Witida Laopajon,Watchara Kasinrerk,Ponlatham Chaiyarit,Supansa Pata
Background Human trefoil factor (TFF) peptides consist of three members: TFF1, TFF2 and TFF3. TFF3 is the most abundant TFF peptide in saliva. TFF3 homodimer was suggested to be involved in apoptosis inhibition and malignancy. Determination of TFF3 homodimer expression profiles in saliva may lead to new information about oral biology and diseases. The objective of this study was to generate monoclonal
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SV40 Large T Antigen Disrupts Embryogenesis of Canine and Porcine Somatic Cell Nuclear Transfer Embryo. Biol. Proced. Online (IF 2.711) Pub Date : 2017-10-28 Kiyoung Eun,Seon-Ung Hwang,Yeon Woo Jeong,Sunyoung Seo,Seon Yong Lee,Woo Suk Hwang,Sang-Hwan Hyun,Hyunggee Kim
BACKGROUND Somatic cell nuclear transfer (SCNT) is a useful biotechnological tool for transgenic animal production using genetically modified somatic cells (GMSCs). However, there are several limitations preventing successful transgenic animal generation by SCNT, such as obtaining proper somatic donor cells with a sufficiently long life span and proliferative capacity for generating GMSCs. Here, we
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Enhanced Mutant Screening in One-step PCR-based Multiple Site-directed Plasmid Mutagenesis by Introduction of Silent Restriction Sites for Structural and Functional Study of Proteins. Biol. Proced. Online (IF 2.711) Pub Date : 2017-09-30 Ting-Yu Kuo,Chung-Che Tsai,Hua-Wen Fu
Site-directed mutagenesis (SDM) has been widely used for studying the structure and function of proteins. A one-step polymerase chain reaction (PCR)-based multiple site-directed plasmid mutagenesis method with extended non-overlapping sequence at the 3' end of the primer increases the PCR amplification efficiency and the capacity of multi-site mutagenesis. Here, we introduced silent restriction sites
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Efficient and inexpensive transient expression of multispecific multivalent antibodies in Expi293 cells. Biol. Proced. Online (IF 2.711) Pub Date : 2017-09-22 Xiaotian T Fang,Dag Sehlin,Lars Lannfelt,Stina Syvänen,Greta Hultqvist
BACKGROUND Immunotherapy is a very fast expanding field within drug discovery and, hence, rapid and inexpensive expression of antibodies would be extremely valuable. Antibodies are, however, difficult to express. Multifunctional antibodies with additional binding domains further complicate the expression. Only few protocols describe the production of tetravalent bispecific antibodies and all with limited
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An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue. Biol. Proced. Online (IF 2.711) Pub Date : 2017-09-01 Sarah-Anne David,Benoît Piégu,Christelle Hennequet-Antier,Maëlle Pannetier,Tiphaine Aguirre-Lavin,Sabine Crochet,Thierry Bordeau,Nathalie Couroussé,Aurélien Brionne,Yves Bigot,Anne Collin,Vincent Coustham
BACKGROUND Genomic loci associated with histone marks are typically analyzed by immunoprecipitation of the chromatin followed by quantitative-PCR (ChIP-qPCR) or high throughput sequencing (ChIP-seq). Chromatin can be either cross-linked (X-ChIP) or used in the native state (N-ChIP). Cross-linking of DNA and proteins helps stabilizing their interactions before analysis. Despite X-ChIP is the most commonly
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Cell Counting and Viability Assessment of 2D and 3D Cell Cultures: Expected Reliability of the Trypan Blue Assay. Biol. Proced. Online (IF 2.711) Pub Date : 2017-08-18 Filippo Piccinini,Anna Tesei,Chiara Arienti,Alessandro Bevilacqua
BACKGROUND Whatever the target of an experiment in cell biology, cell counting and viability assessment are always computed. The Trypan Blue (TB) assay was proposed about a century ago and is still the most widely used method to perform cell viability analysis. Furthermore, the combined use of TB with a haemocytometer is also considered the standard approach to estimate cell population density. There
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An Initial Investigation of an Alternative Model to Study rat Primordial Germ Cell Epigenetic Reprogramming. Biol. Proced. Online (IF 2.711) Pub Date : 2017-08-09 Isabelle Hernandez Cantão,Renato Borges Tesser,Taiza Stumpp
BACKGROUND Primordial germ cells (PGC) are the precursors of the gametes. During pre-natal development, PGC undergo an epigenetic reprogramming when bulk DNA demethylation occurs and is followed by sex-specific de novo methylation. The de novo methylation and the maintenance of the methylation patterns depend on DNA methyltransferases (DNMTs). PGC reprogramming has been widely studied in mice but not
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3D Printer Generated Tissue iMolds for Cleared Tissue Using Single- and Multi-Photon Microscopy for Deep Tissue Evaluation. Biol. Proced. Online (IF 2.711) Pub Date : 2017-07-12 Sean J Miller,Jeffrey D Rothstein
BACKGROUND Pathological analyses and methodology has recently undergone a dramatic revolution. With the creation of tissue clearing methods such as CLARITY and CUBIC, groups can now achieve complete transparency in tissue samples in nano-porous hydrogels. Cleared tissue is then imagined in a semi-aqueous medium that matches the refractive index of the objective being used. However, one major challenge
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Pre-Microporation Improves Outcome of Pancreatic Islet Labelling for Optical and 19F MR Imaging. Biol. Proced. Online (IF 2.711) Pub Date : 2017-07-05 Vít Herynek,Andrea Gálisová,Mangala Srinivas,Eric A W van Dinther,Lucie Kosinová,Jiri Ruzicka,Markéta Jirátová,Jan Kriz,Daniel Jirák
BACKGROUND In vitro labelling of cells and small cell structures is a necessary step before in vivo monitoring of grafts. We modified and optimised a procedure for pancreatic islet labelling using bimodal positively charged poly(lactic-co-glycolic acid) nanoparticles with encapsulated perfluoro crown ethers and indocyanine green dye via microporation and compared the method with passive endocytosis
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Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs. Biol. Proced. Online (IF 2.711) Pub Date : 2017-06-10 Xiao-Long Yuan,Zhe Zhang,Rong-Yang Pan,Ning Gao,Xi Deng,Bin Li,Hao Zhang,Per Torp Sangild,Jia-Qi Li
BACKGROUND Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of
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Comparison of transepithelial resistance measurement techniques: Chopsticks vs. Endohm. Biol. Proced. Online (IF 2.711) Pub Date : 2017-05-12 Rebecca A Sheller,Maria E Cuevas,Maria C Todd
BACKGROUND TER measurements across confluent cellular monolayers provide a useful indication of TJ strength between epithelial and endothelial cells in culture. Having a reliable and accurate method of measuring cell-to-cell adhesion is critical to studies in pathophysiology and cancer metastasis. However, the use of different technical approaches to measure TER has reportedly yielded inconsistent
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LncRNAs and immunity: watchdogs for host pathogen interactions. Biol. Proced. Online (IF 2.711) Pub Date : 2017-05-04 Peerzada Tajamul Mumtaz,Shakil Ahmad Bhat,Syed Mudasir Ahmad,Mashooq Ahmad Dar,Raashid Ahmed,Uneeb Urwat,Aadil Ayaz,Divya Shrivastava,Riaz Ahmad Shah,Nazir Ahmad Ganai
Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction
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Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer. Biol. Proced. Online (IF 2.711) Pub Date : 2017-03-24 Yan Lu,Shulin/Sl Li,Shiguo/Sg Zhu,Yabin/Yb Gong,Jun/J Shi,Ling/L Xu
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection
更新日期:2019-11-01